Jeffrey L. Blanchard

Assistant Professor of Biology, University of Massachusetts


Ph.D.: Botany, University of Georgia

Microbial cellular and community networks; influence of environmental change on the evolution of molecular processes; systems biology; bioinformatics

We use systems-level approaches to understand bacterial stress response networks related to host-pathogen interactions and the influence of global climate change on populations of marine cyanobacteria and communities of bacteria. Our research program is characterized by a synergistic integration of computation, experiment and theory and we welcome new people from different academic disciplines. There are three fundamental aspects of our research; (1) Effectively utilize genomic data from different sources to discover functions for genes and proteins. (2) Uncover rules governing and constraining biological systems. (3) Enable predictive models of biological systems that incorporate biochemical and genetic data. Here are some of our project areas for systems research.

The effects of global climate change on populations of marine cyanobacteria

Global climate change is an international problem that already is impacting the evolutionary trajectory of our planet's biota. In spite of the widely appreciated magnitude of this problem, we still have a limited ability to estimate current and long-term biological effects. As the most numerically dominant species in the ocean, Prochlorococcus has become a central object of study for understanding carbon fixation by photosynthetic organisms. Prochlorococcus is very unusual for a free living organism in that it show signs of reductive genome evolution that are typically found in organelles, endosymbionts and pathogens (see Blanchard et al. 2000) and now has a minimal transcriptional regulator network for sensing environmental change. The long-term goal of our research is to integrate large-scale “genomic” data sets into probabilistic models that allow inferences and decisions regarding the trajectory of photosynthetic organisms in a changing global climate. Towards this goal we are working on;

• Integrating genome sequence and expression microarray data into models that allow us to identify process and subnetworks subject to different selective pressures related to changes in ocean chemistry.
• Developing and applying statistical methods to identify regulatory motifs and their relative binding strength in sequence data using a combination of microarray and sequence data (In collaboration with Erin Conlon).

Stress response networks in enteric bacteria (In collaboration with Pablo Pomposiello)

Signals initiated by diverse factors involved in host pathogen interactions, including antibiotics and nitric oxide, are funneled by three dissimilar sensor transcriptional regulators (SoxR, MarR and RamR) to three homologous transcriptional activators (SoxS, MarA and RamA) to regulate a similar but not completely overlapping set of genes coding for key metabolic control points and defense mechanisms. This unusual regulatory circuit design was assembled fairly recently in the ancestor of Escherichia, Salmonella and Klebsiella and soxS, marA and ramA are derived from duplications events that occurred around this time. Because, these transcriptional activators historically bound the same set of genes we are using comparative experimental and computational approaches for determining the regulatory network structure and creating models that describe the response of the bacteria to host and other environmental factors.

Microbial environmental and community genomics

Most microbes are currently impossible to grow in the laboratory. New approaches are being developed to sequence genomes of microbes straight from environmental samples obviating the need to first culture microbes. One spectacular application of this evolving technology was to a microbial community in the Sargasso Sea (Venter et al. 2004). The published data set included at least 1800 bacterial species many which have not been previously described. Fortunately for us there is also a lot of sequence data on marine cyanobacteria, particularly Prochlorococcus marinus. We have developed a new method for separating genomes from cocultures of bacteria (in collaboration with Derek Lovely) and are applying the methods to the Sargasso Sea and other environmental sequencing data sets. We are also interested in developing methods that utilize variation in DNA sequences to understand microbial population dynamics and methods for building a conceptual model of the interactions among various members of these communities.

Representative publications:

Sun, Z., Blanchard, J.L. 2014. Strong genome-wide selection early in the evolution of Prochlorococcus resulted in a reduced genome through the loss of a large number of small effect genes. PLOS ONE, Mar 3;9(3): e88837.

Mukherjee, S., Thompson, L.K., Godin, S., Schackwitz, W., Lipzen, A., Martin, J., Blanchard, J.L. 2014. Population level analysis of evolved mutations underlying improvements in plant cellulose and hemicellulose fermentation by Clostridium phytofermentans. PLOS ONE, 9(1): e86731.

Biddle, A.S., Black, S.J., Blanchard, J.L. 2013. An in vitro model of the horse gut microbiome enables identification of lactate-utilizing bacteria that differentially respond to starch induction. PLOS ONE, PLoS ONE 8(10): e77599

Abdul-Rahman, F., Petit, E., Blanchard, J.L. 2013. The Distribution of Polyhedral Bacterial Microcompartments Suggests Frequent Horizontal Transfer and Operon Reassembly. J. Phylogen. Evolution. Biol., 1: e118.

Biddle, A.S., Stewart, L., Blanchard, J.L., Leschine, S.B. 2013. Untangling the Genetic Basis of Fibrolytic Specialization by Lachnospiraceae and Ruminococcaceae in Diverse Gut Communities. Diversity, 5(3), 627-640.

Tolonen, A.C., Petit, E., Blanchard, J.L., Warnick, T., Leschine, S.B. 2013. "Technologies to Study Plant Biomass Fermentation using the Model Bacterium Clostridium phytofermentans." Chapt 7 (pp 114-139) in "Biological Conversion of Biomass for Fuels and Chemicals: Explorations from Natural Utilization Systems". Edited by Jianzhong Sun, Shi-You Ding and Joy Peterson. The Royal Society of Chemistry.

Petit, E., Latouf, W., Coppi, M., Currie, D., Rhomasko, I., Desphande, S., Haas, K., Alvelo-Maurosa, J.G., Wardman, C., Schnell, D., Leschine, L., Blanchard, J. 2013. Involvement of a bacterial microcompartment in the metabolism of fucose and rhamnose by Clostridium phytofermentans. PLoS One, 8(1): e54337.

Damery, D., Hayes, J., Blanchard, J.L. 2010. The potential for production of ethanol from woody biomass by the microbe Clostridium phytofermentans. Wood Structures and Properties '10. Edited by Kúdela and Laga?a. Arbora Publishers. p21-25.

Hu, J., Blanchard, J.L. 2009. Environmental sequence data from the Sargasso Sea reveal that the characteristics of genome reduction in Prochlorococcus are not a harbinger for an escalation in genetic drift. Molecular Biology and Evolution, Jan;26(1): 5-13.

Lu, S., Becker, K.A., Hagen, M.J., Yan, H., Roberts, A.L., Mathews, L.A., Schneider, S.S., Siegelmann, H.T., Macbeth, K.J., Tirrell, S.M., Blanchard, J.L., Jerry, D.J. 2008. Transcriptional Responses to Estrogen and Progesterone in Mammary Gland Identify Networks Regulating p53 Activity. Endocrinology, Oct;149(10): 4809-20. Epub 2008 Jun 12.

Blanchard, J.L., Chen, W., Conlon, E.M., Pomposiello, P.J. 2007. Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks. PLoS ONE, 2(11): e1186.

Conlon, E.M., Alpargu, G., Blanchard, J.L. 2006. Comparative genomics approaches for identifying genetic regulatory networks. Chance, 19:45-48.

Richards, T.A., Dacks, J.B., Campbell, S.A., Blanchard, J.L., Foster, P.G., McLeod, R., Roberts, C.W. 2006. Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements. Eukaryot Cell, 5: 1517-31.

Blanchard JL (2004) Bioinformatics and Systems Biology, rapidly evolving tools for interpreting plant response to global change. Field Crops Research. 90:117-131.

De Visser AJM, Hermisson J, Wagner, GP, Ancel LW, Bagheri-Chaichian H, Blanchard JL, Chao L, Cheverud JM, Elena SF, Fontana W, Gibson G, Hansen TF, Krakauer D, Lewontin RC, Ofria C, Rice SH, von Dassow G, Wagner A, Whitlock MC (2003) Perspective: Evolution and detection of genetic robustness. Evolution. 57:1959-1972.

Kuffner RM, Gonzales M, Steadman P, Wlodek DK, Jankowitz RJ, Boinoff JR, Montoya AL, Peterson TF, Bulmore DL, Blanchard JL (2002) PathDB. Nucleic Acids Research Database Issue.

Brinkman FSL, Blanchard JL, Greberg H, Wan I, De Koning A, Av-Gay Y, Brunham RC, Fernandez RC, Finlay BB, Otto SP, Ouellette BF, Keeling P, Hancock REW, Rose AM, SJM Jones (2002) Plant-like genes in Chlamydia species reflect Chlamydia's ancestral relationship with cyanobacteria and the chloroplast. Genome Research. 12 :1159-67

Blanchard JL, Lynch M (2000) Why do organellar genes end up in the nucleus? Trends in Genetics. 16 :315-320.

De Visser AJM, Zeyl CW, Gerrish PJ, Blanchard JL, Lenski RE (1999) Diminishing returns from mutation supply rate in asexual populations. Science. 283 :404-406.

Lynch M, Blanchard JL, Houle D, Kibota T, Schultz S, Vassileva L, Willis J (1999) Spontaneous deleterious mutation. Evolution. 53 :645-663.

Blanchard JL, Hicks JS (1999) The non-photosynthetic plastid in malarial parasites and other apicomplexans is derived from outside the green plastid lineage. Journal of Eukaryotic Microbiology. 46 :367-375.